التفاصيل البيبلوغرافية
العنوان:
SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2
المؤلفون:
Eales, O , Page, AJ , de Oliveira Martins, L , Wang, H , Bodinier, B , Haw, D , Jonnerby, J , Atchison, C , Robson, SC , Connor, TR , Loman, NJ , Golubchik, T , Nunez, RTM , Bonsall, D , Rambaut, A , Snell, LB , Livett, R , Ludden, C , Corden, S , Nastouli, E , Nebbia, G , Johnston, I , Lythgoe, K , Torok, ME , Goodfellow, IG , Prieto, JA , Saeed, K , Jackson, DK , Houlihan, C , Frampton, D , Hamilton, WL , Witney, AA , Bucca, G , Pope, CF , Moore, C , Thomson, EC , Harrison, EM , Smith, CP , Rogan, F , Beckwith, SM , Murray, A , Singleton, D , Eastick, K , Sheridan, LA , Randell, P , Jackson, LM , Ariani, CV , Gonçalves, S , Fairley, DJ , Loose, MW , Watkins, J , Moses, S , Nicholls, S , Bull, M , Amato, R , Smith, DL , Aanensen, DM , Barrett, JC , Aggarwal, D , Shepherd, JG , Curran, MD , Parmar, S , Parker, MD , Williams, C , Glaysher, S , Underwood, AP , Bashton, M , Pacchiarini, N , Loveson, KF , Byott, M , Carabelli, AM , Templeton, KE , de Silva, TI , Wang, D , Langford, CF , Sillitoe, J , Gunson, RN , Cottrell, S , O’Grady, J , Kwiatkowski, D , Lillie, PJ , Cortes, N , Moore, N , Thomas, C , Burns, PJ , Mahungu, TW , Liggett, S , Beckett, AH , Holden, MTG , Levett, LJ , Osman, H , Hassan-Ibrahim, MO , Simpson, DA , Chand, M , Gupta, RK , Darby, AC , Paterson, S , Pybus, OG , Volz, EM , de Angelis, D , Robertson, DL , Martincorena, I , Aigrain, L , Bassett, AR , Wong, N , Taha, Y , Erkiert, MJ , Chapman, MHS , Dewar, R , McHugh, MP , Mookerjee, S , Aplin, S , Harvey, M , Sass, T , Umpleby, H , Wheeler, H , McKenna, JP , Warne, B , Taylor, JF , Chaudhry, Y , Izuagbe, R , Jahun, AS , Young, GR , McMurray, C , McCann, CM , Nelson, A , Elliott, S , Lowe, H , Price, A , Crown, MR , Rey, S , Roy, S , Temperton, B , Shaaban, S , Hesketh, AR , Laing, KG , Monahan, IM , Heaney, J , Pelosi, E , Silviera, S , Wilson-Davies, E , Fryer, H , Adams, H , du Plessis, L , Johnson, R , Harvey, WT , Hughes, J , Orton, RJ , Spurgin, LG , Bourgeois, Y , Ruis, C , O’Toole, Á , Gourtovaia, M , Sanderson, T , Fraser, C , Edgeworth, J , Breuer, J , Michell, SL , Todd, JA , John, M , Buck, D , Gajee, K , Kay, GL , Peacock, SJ , Heyburn, D , Kitchman, K , McNally, A , Pritchard, DT , Dervisevic, S , Muir, P , Robinson, E , Vipond, BB , Ramadan, NA , Jeanes, C , Weldon, D , Catalan, J , Jones, N , da Silva Filipe, A , Fuchs, M , Miskelly, J , Jeffries, AR , Oliver, K , Park, NR , Ash, A , Koshy, C , Barrow, M , Buchan, SL , Mantzouratou, A , Clark, G , Holmes, CW , Campbell, S , Davis, T , Tan, NK , Brown, JR , Harris, KA , Kidd, SP , Grant, PR , Xu-McCrae, L , Cox, A , Madona, P , Pond, M , Randell, PA , Withell, KT , Graham, C , Denton-Smith, R , Swindells, E , Turnbull, R , Sloan, TJ , Bosworth, A , Hutchings, S , Pymont, HM , Casey, A , Ratcliffe, L , Jones, CR , Knight, BA , Haque, T , Hart, J , Irish-Tavares, D , Witele, E , Mower, C , Watson, LK , Collins, J , Eltringham, G , Crudgington, D , Macklin, B , Iturriza-Gomara, M , Lucaci, AO , McClure, PC , Carlile, M , Holmes, N , Storey, N , Rooke, S , Yebra, G , Craine, N , Perry, M , Alikhan, N - F , Bridgett, S , Cook, KF , Fearn, C , Goudarzi, S , Lyons, RA , Williams, T , Haldenby, ST , Durham, J , Leonard, S , Davies, RM , Batra, R , Blane, B , Spyer, MJ , Smith, P , Yavus, M , Williams, RJ , Mahanama, AIK , Samaraweera, B , Girgis, ST , Hansford, SE , Green, A , Beaver, C , Bellis, KL , Dorman, MJ , Kay, S , Prestwood, L , Rajatileka, S , Quick, J , Poplawski, R , Reynolds, N , Mack, A , Morriss, A , Whalley, T , Patel, B , Georgana, I , Hosmillo, M , Pinckert, ML , Stockton, J , Henderson, JH , Hollis, A , Stanley, W , Yew, WC , Myers, R , Thornton, A , Adams, A , Annett, T , Asad, H , Birchley, A , Coombes, J , Evans, JM , Fina, L , Gatica-Wilcox, B , Gilbert, L , Graham, L , Hey, J , Hilvers, E , Jones, S , Jones, H , Kumziene-Summerhayes, S , McKerr, C , Powell, J , Pugh, G , Taylor, S , Trotter, AJ , Williams, CA , Kermack, LM , Foulkes, BH , Gallis, M , Hornsby, HR , Louka, SF , Pohare, M , Wolverson, P , Zhang, P , MacIntyre-Cockett, G , Trebes, A , Moll, RJ , Ferguson, L , Goldstein, EJ , Maclean, A , Tomb, R , Starinskij, I , Thomson, L , Southgate, J , Kraemer, MUG , Raghwani, J , Zarebski, AE , Boyd, O , Geidelberg, L , Illingworth, CJ , Jackson, C , Pascall, D , Vattipally, S , Freeman, TM , Hsu, SN , Lindsey, BB , James, K , Lewis, K , Tonkin-Hill, G , Tovar-Corona, JM , Cox, MG , Abudahab, K , Menegazzo, M , MEng, BEWT , Yeats, CA , Mukaddas, A , Wright, DW , Colquhoun, R , Hill, V , Jackson, B , McCrone, JT , Medd, N , Scher, E , Keatley, J - P , Curran, T , Morgan, S , Maxwell, P , Smith, K , Eldirdiri, S , Kenyon, A , Holmes, AH , Price, JR , Wyatt, T , Mather, AE , Skvortsov, T , Hartley, JA , Guest, M , Kitchen, C , Merrick, I , Munn, R , Bertolusso, B , Lynch, J , Vernet, G , Kirk, S , Wastnedge, E , Stanley, R , Idle, G , Bradley, DT , Poyner, J , Mori, M , Jones, O , Wright, V , Brooks, E , Churcher, CM , Fragakis, M , Galai, K , Jermy, A , Judges, S , McManus, GM , Smith, KS , Westwick, E , Attwood, SW , Bolt, F , Davies, A , De Lacy, E , Downing, F , Edwards, S , Meadows, L , Jeremiah, S , Smith, N , Foulser, L , Charalampous, T , Patel, A , Berry, L , Boswell, T , Fleming, VM , Howson-Wells, HC , Joseph, A , Khakh, M , Lister, MM , Bird, PW , Fallon, K , Helmer, T , McMurray, CL , Odedra, M , Shaw, J , Tang, JW , Willford, NJ , Blakey, V , Raviprakash, V , Sheriff, N , Williams, L - A , Feltwell, T , Bedford, L , Cargill, JS , Hughes, W , Moore, J , Stonehouse, S , Atkinson, L , Lee, JCD , Shah, D , Alcolea-Medina, A , Ohemeng-Kumi, N , Ramble, J , Sehmi, J , Williams, R , Chatterton, W , Pusok, M , Everson, W , Castigador, A , Macnaughton, E , Bouzidi, KE , Lampejo, T , Sudhanva, M , Breen, C , Sluga, G , Ahmad, SSY , George, RP , Machin, NW , Binns, D , James, V , Blacow, R , Coupland, L , Smith, L , Barton, E , Padgett, D , Scott, G , Cross, A , Mirfenderesky, M , Greenaway, J , Cole, K , Clarke, P , Duckworth, N , Walsh, S , Bicknell, K , Impey, R , Wyllie, S , Hopes, R , Bishop, C , Chalker, V , Harrison, I , Gifford, L , Molnar, Z , Auckland, C , Evans, C , Johnson, K , Partridge, DG , Raza, M , Baker, P , Bonner, S , Essex, S , Murray, LJ , Lawton, AI , Burton-Fanning, S , Payne, BAI , Waugh, S , Gomes, AN , Kimuli, M , Murray, DR , Ashfield, P , Dobie, D , Ashford, F , Best, A , Crawford, L , Cumley, N , Mayhew, M , Megram, O , Mirza, J , Moles-Garcia, E , Percival, B , Driscoll, M , Ensell, L , Lowe, HL , Maftei, L , Mondani, M , Chaloner, NJ , Cogger, BJ , Easton, LJ , Huckson, H , Lewis, J , Lowdon, S , Malone, CS , Munemo, F , Mutingwende, M , Nicodemi, R , Podplomyk, O , Somassa, T , Beggs, A , Richter, A , Cormie, C , Dias, J , Forrest, S , Higginson, EE , Maes, M , Young, J , Davidson, RK , Jackson, KA , Turtle, L , Keeley, AJ , Ball, J , Byaruhanga, T , Chappell, JG , Dey, J , Hill, JD , Park, EJ , Fanaie, A , Hilson, RA , Yaze, G , Lo, S , Afifi, S , Beer, R , Maksimovic, J , McCluggage, K , Spellman, K , Bresner, C , Fuller, W , Marchbank, A , Workman, T , Shelest, E , Debebe, J , Sang, F , Zamudio, ME , Francois, S , Gutierrez, B , Vasylyeva, TI , Flaviani, F , Ragonnet-Cronin, M , Smollett, KL , Broos, A , Mair, D , Nichols, J , Nomikou, K , Tong, L , Tsatsani, I , O’Brien, PS , Rushton, S , Sanderson, R , Perkins, J , Cotton, S , Gallagher, A , Allara, E , Pearson, C , Bibby, D , Dabrera, G , Ellaby, N , Gallagher, E , Hubb, J , Lackenby, A , Lee, D , Manesis, N , Mbisa, T , Platt, S , Twohig, KA , Morgan, M , Aydin, A , Baker, DJ , Foster-Nyarko, E , Prosolek, SJ , Rudder, S , Baxter, C , Carvalho, SF , Lavin, D , Mariappan, A , Radulescu, C , Singh, A , Tang, M , Morcrette, H , Bayzid, N , Cotic, M , Balcazar, CE , Gallagher, MD , Maloney, D , Stanton, TD , Williamson, KA , Manley, R , Michelsen, ML , Sambles, CM , Studholme, DJ , Warwick-Dugdale, J , Eccles, R , Gemmell, M , Gregory, R , Hughes, M , Nelson, C , Rainbow, L , Vamos, EE , Webster, HJ , Whitehead, M , Wierzbicki, C , Angyal, A , Green, LR , Whiteley, M , Betteridge, E , Bronner, IF , Farr, BW , Goodwin, S , Lensing, SV , McCarthy, SA , Quail, MA , Rajan, D , Redshaw, NM , Scott, C , Shirley, L , Thurston, SAJ , Rowe, W , Gaskin, A , Le-Viet, T , Bonfield, J , Liddle, J , Whitwham, A , Ashby, D , Barclay, W , Taylor, G , Cooke, G , Ward, H , Darzi, A , Riley, S , Chadeau-Hyam, M , Donnelly, CA , Elliott, P , The COVID-19 Genomics UK (COG-UK) Consortium
المساهمون:
Department of Health, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), Cancer Research UK, Commission of the European Communities, Wellcome Trust, National Institute for Health Research, Imperial College Healthcare NHS Trust: Research Capability Funding (RCF)
المصدر:
1471-233
بيانات النشر:
BioMed Central, 2022.
سنة النشر:
2022
مصطلحات موضوعية:
Delta variant , Science & Technology , SARS-CoV-2 , COVID-19 , 1103 Clinical Sciences , C500 , Microbiology , Genetic diversity , B900 , Infectious Diseases , England , COVID-19 Genomics UK (COG-UK) Consortium , 1108 Medical Microbiology , Mutation , Humans , Transmission advantage , Life Sciences & Biomedicine , Phylogeny , 0605 Microbiology
الوصف:
Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
وصف الملف:
application/pdf; text
تدمد:
1471-2334
الوصول الحر:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::30139e4e840bd988c0b91755bedc8f1dTest http://hdl.handle.net/10044/1/98322Test
حقوق:
OPEN
رقم الانضمام:
edsair.doi.dedup.....30139e4e840bd988c0b91755bedc8f1d
قاعدة البيانات:
OpenAIRE
